Isotropic 3D electron microscopy reference library of whole cells and tissues

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by imaging whole cells and tissues with enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) in high resolution with month-long acquisition duration. We use this approach to generate reference 3D image datasets at 4-nm isotropic voxels for ten different examples, including cultured cells (cancer, macrophages, and T-cells) as well as tissues (mouse pancreatic islets and the Drosophila fan-shaped body). We open access to all datasets in OpenOrganelle, an interactive web platform that allows accessing both the original 3D EM data, and subsequent organelle segmentation. Together, these data will serve as a reference library to explore comprehensive quantification of whole cells and their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.